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Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System.
Forensic Sci Int Genet. 2017 11; 31:135-148.FS

Abstract

The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples). Results showed that quantitative polymerase chain reaction (qPCR)-based sample quantification and library normalization and the appropriate number of pooled libraries and concentration of diluted libraries provided a greater level of MPS performance and repeatability. Repeatable and concordant genotypes were obtained by the ForenSeq Kit. Full profiles were obtained from ≥100pg input DNA for STRs and ≥200pg for SNPs. A sample with ≥5% minor contributors was considered as a mixture by imbalanced allele coverage ratio distribution, and full profiles from minor contributors were easily detected between 9:1 and 1:9 mixtures with known reference profiles. The ForenSeq Kit tolerated considerable concentrations of inhibitors like ≤200μM hematin and ≤50μg/ml humic acid, and >56% STR profiles and >88% SNP profiles were obtained from ≥200-bp degraded samples. Also, it was adapted to case-type samples. As a whole, the ForenSeq Kit is a well-performed, robust, reliable, reproducible and highly informative assay, and it can fully meet requirements for human identification. Further, sensitive QC indicator and automated sample comparison function in the ForenSeq™ Universal Analysis Software are quite helpful, so that we can concentrate on questionable genotypes and avoid tedious and time-consuming labor to maximum the time spent in data analysis.

Authors+Show Affiliations

Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang 110854, Liaoning, PR China. Electronic address: nevergfaye@gmail.com.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang 110032, Liaoning, PR China.Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang 110854, Liaoning, PR China.Department of Forensic Medicine, Criminal Investigation Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang 110854, Liaoning, PR China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

28938154

Citation

Guo, Fei, et al. "Massively Parallel Sequencing of Forensic STRs and SNPs Using the Illumina® ForenSeq™ DNA Signature Prep Kit On the MiSeq FGx™ Forensic Genomics System." Forensic Science International. Genetics, vol. 31, 2017, pp. 135-148.
Guo F, Yu J, Zhang L, et al. Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System. Forensic Sci Int Genet. 2017;31:135-148.
Guo, F., Yu, J., Zhang, L., & Li, J. (2017). Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System. Forensic Science International. Genetics, 31, 135-148. https://doi.org/10.1016/j.fsigen.2017.09.003
Guo F, et al. Massively Parallel Sequencing of Forensic STRs and SNPs Using the Illumina® ForenSeq™ DNA Signature Prep Kit On the MiSeq FGx™ Forensic Genomics System. Forensic Sci Int Genet. 2017;31:135-148. PubMed PMID: 28938154.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System. AU - Guo,Fei, AU - Yu,Jiao, AU - Zhang,Lu, AU - Li,Jun, Y1 - 2017/09/08/ PY - 2017/02/12/received PY - 2017/08/06/revised PY - 2017/09/06/accepted PY - 2017/9/25/pubmed PY - 2017/12/12/medline PY - 2017/9/23/entrez KW - Evaluation KW - ForenSeq™ DNA Signature Prep Kit KW - Massively parallel sequencing (MPS) KW - MiSeq FGx(TM) Forensic Genomics System KW - Short tandem repeat (STR) KW - Single nucleotide polymorphism (SNP) SP - 135 EP - 148 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 31 N2 - The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples). Results showed that quantitative polymerase chain reaction (qPCR)-based sample quantification and library normalization and the appropriate number of pooled libraries and concentration of diluted libraries provided a greater level of MPS performance and repeatability. Repeatable and concordant genotypes were obtained by the ForenSeq Kit. Full profiles were obtained from ≥100pg input DNA for STRs and ≥200pg for SNPs. A sample with ≥5% minor contributors was considered as a mixture by imbalanced allele coverage ratio distribution, and full profiles from minor contributors were easily detected between 9:1 and 1:9 mixtures with known reference profiles. The ForenSeq Kit tolerated considerable concentrations of inhibitors like ≤200μM hematin and ≤50μg/ml humic acid, and >56% STR profiles and >88% SNP profiles were obtained from ≥200-bp degraded samples. Also, it was adapted to case-type samples. As a whole, the ForenSeq Kit is a well-performed, robust, reliable, reproducible and highly informative assay, and it can fully meet requirements for human identification. Further, sensitive QC indicator and automated sample comparison function in the ForenSeq™ Universal Analysis Software are quite helpful, so that we can concentrate on questionable genotypes and avoid tedious and time-consuming labor to maximum the time spent in data analysis. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/28938154/Massively_parallel_sequencing_of_forensic_STRs_and_SNPs_using_the_Illumina®_ForenSeq™_DNA_Signature_Prep_Kit_on_the_MiSeq_FGx™_Forensic_Genomics_System_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30189-8 DB - PRIME DP - Unbound Medicine ER -